rs2919024

chr1-242358740-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001372062.1(PLD5):c.190-10498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 152,290 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.021 (50 hom., cov: 31)
• Consequence: PLD5 NM_001372062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

PLD5 (HGNC:26879): (phospholipase D family member 5) Predicted to enable catalytic activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0212 (3230/152290) while in subpopulation EAS AF= 0.0326 (169/5180). AF 95% confidence interval is 0.0311. There are 50 homozygotes in gnomad4. There are 1553 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLD5	NM_001372062.1	c.190-10498T>C		intron_variant		ENST00000536534.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLD5	ENST00000536534.7	c.190-10498T>C		intron_variant		1	NM_001372062.1	P1

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3222 AN: 152172 Hom.: 51 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0212 AC: 3230 AN: 152290 Hom.: 50 Cov.: 31 AF XY: 0.0209 AC XY: 1553 AN XY: 74452

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.0166

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.00301

Gnomad4 NFE AF: 0.0145

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0191 Hom.: 8

Bravo AF: 0.0235

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.0
Dann	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2919024; hg19: chr1-242522042;